Advanced settings

Fetching from a bam file

Margin around a variant or manually entered coordinate where reads will be pulled from a bam file (use this parameter carefully as importing too much data can crash your web browser due to memory overload)

bp

Automation

Make Ribbon automatically go to each variant in a bedpe file and take pictures of the multi-read view and a selection of reads. Instructions: Load a bedpe file and a bam file first, set the settings below and in the right-side panel as you want them and click Run!

Prefix for image files

Number of reads to take pictures of (randomly selected)

Print variant coordinates onto multi-read view

Download a file with info and coordinates for each variant alongside the images

Only select reads with alignments that start or end near the bedpe variant

Distance:

Information about Ribbon

Ribbon is made by Maria Nattestad with support from Pacific Biosciences and Cold Spring Harbor Laboratory.

Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right.

Make sure the bam file exists and that it has a corresponding index (.bai or .csi) file with an identical filename except for the addition of the .bai or .csi suffix. If the bam file does not exist or cannot be read, a header will fail to appear but there will be no error message. If the header of the bam file does not show up within about 10 seconds, loading the bam file has probably failed and you should check to make sure it actually exists at the given address. (To test for this, put the url into your web browser. If it starts downloading the bam file, then also check whether adding .bai or .csi to the url downloads the index file. If one of these does not start a download, then the file does not exist.)

Note that the bam file does not get read into memory, but the index file does, so if the index file is huge, it will take a while the first time you fetch reads from the bam file.

Showing only the first 30 variants. Sort by clicking column names, and filter by typing into the text boxes for each column. For instance, type >20 or =chr2. Separate multiple filters in a single column using spaces. For bam files, click on a row in the table to fetch reads around that feature.